Cyclic nucleotide phosphodiesterase (PDE), that is a multigenic enzyme superfamily ubiquitously distributed in mammalians, mainly contributes to intracellular signaling regulation. Its various isozymes specifically control in a spatio-temporal manner intracellular levels of cAMP and cGMP downstream receptor activation and nearby functional proteins. The PDE superfamily is constituted by 11 gene families (PDE1-PDE11), comprising 21 genes represented by more than 100 mRNA products due to alternative splicing. Among them, PDE3, PDE4 and PDE5 were viewed as therapeutic targets and therefore, due to the successful development of Viagra™ (sildenafil, potent selective PDE5 inhibitor), the knowledge in PDE field burst out with the help of academic/pharmaceutical collaborations. Organic medicinal chemistry, using crystallographic and docking approaches, has focused its search on the catalytic pocket of PDEs, leaving aside the development of variant subtype specific PDE inhibitors and activators. This review firstly describes the various properties of each PDE isozyme, focusing particularly on their regulatory domains, mainly located in the N-terminus. Thereafter, we review the possible peptidic regulations of PDE activity itself, then the PDE anchoring in macromolecular complexes and finally the direct interaction of PDE with some critical intracellular proteins, such as β-arrestin, immunophilin and proteins containing SH3-domain. Altogether, it appears that a peptidic approach would be helpful to study the intrinsic PDE regulation of each subfamily, and thereafter the PDE peptidic motifs implicated as well as PDE location in signaling cascades. Taking in account the various regulatory PDE domains could lead to design new peptides to conceive variant specific inhibitors as well as activators in a therapeutical goal.